are you sure about two different ones? both RB and BL only list two of the same part in the set...

Yes, I’m sure. I bought both base plates from the set on eBay. At first, I also assumed that the plates were identical or symmetrical and started working with just one part. But during the “assembly” (both plates with the lava pattern) I noticed that the stripes in the middle don’t line up — they form more of a zigzag pattern. I then took a closer look at the plates and the prints are slightly different. When you assemble each one, the difference is drastic. We need both.

I could imagine that there are just printing differences...
Is it possible to have one part with aligned stripes when there are two facing each other?

It's for sure not a printing issue (like with the other more complex structered basee plates where the position of the individual elemtents slitghty differs). The difference is to large. At least for me. And I guess pad printing is quite precicise. Maybe not with respect to the absolute postion but with respect to the shape of the indidivual elemens itself.
"Is it possible to have one part with aligned stripes when there are two facing each other?" Not sure what you mean. Can you please explain it bit more detailed? Thanks.
I can also upload the scans from the base plates in the LDRAW forum and we can decide if we need two dirffernt ones.

http://www.peeron.com/scans/1349-1/39/
as this is the usage, would it be possible to place an "idealized" print on both halves so that both have the same, symmetric print?